Ns126:Calendar/NOTES/2016-2-24
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Layer specific MHBs with hyper or hypo-MHL[edit]
motivation[edit]
- group tissues of same gem layer
- identify layder specific MHBs with hyper/hypo MHL
Layer specific hyper-MHL regions[edit]
- In total we identified 114 ectoderm-specific MHBs (99 hyper- and 15 hypo-methylated), 75 endoderm specific MHBs (58 hyper and 17 hypo-methylated) and 31 mesoderm specific MHBs (9 hyper and 22 hypo-methylated) (see Methods, Supplementary Table 3).
- Figure saved in laptop: C:\Users\shicheng\Dropbox\Project\methylation\monod\analysis\layer_specfic_mhl
- Raw data saved in Genome-miner: /home/shg047/monod/dec
Rbedtools<-function(functionstring="intersectBed",bed1,bed2,opt.string=""){ #create temp files a.file=tempfile() b.file=tempfile() out =tempfile() options(scipen =99) # not to use scientific notation when writing out #write bed formatted dataframes to tempfile write.table(bed1,file=a.file,quote=F,sep="\t",col.names=F,row.names=F) write.table(bed2,file=b.file,quote=F,sep="\t",col.names=F,row.names=F) # create the command string and call the command using system() command=paste(functionstring,"-a",a.file,"-b",b.file,opt.string,">",out,sep=" ") cat(command,"\n") try(system(command)) res=read.table(out,header=F) unlink(a.file);unlink(b.file);unlink(out) return(res) } cor2bed<-function(cor){ a<-unlist(lapply(strsplit(as.character(cor),split=c(":")),function(x) strsplit(x,"-"))) bed<-matrix(a,ncol=3,byrow=T) return(data.frame(bed)) }
setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl") /home/shg047/monod/dec/Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt data=read.table("/home/shg047/monod/dec/Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt",head=T,sep="\t",as.is=T) head(data) newdata=subset(data,GSI>0.6) table(subset[,2]) mesoderm<-subset(newdata,group=="Mesoderm") ectoderm<-subset(newdata,group=="Ectoderm") endoderm<-subset(newdata,group=="Endoderm") mesodermBed<-cor2bed(mesoderm[,1]) ectodermBed<-cor2bed(ectoderm[,1]) endodermBed<-cor2bed(endoderm[,1]) # change to laptop to plot histgram setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl") data=read.table("Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt",head=T,sep="\t",as.is=T) pdf("hist.layer.specfic.pdf") hist(data[,3],breaks=30,col="green",ylim=c(0,4000),xlab="Layer Specfic Index",main="") dev.off() Rbedtools(functionstring="intersectBed",bed1=mesodermBed,bed2=ectodermBed,opt.string="-wa -u") table<-c(99,66,9) names(table)<-c("Ectoderm","Endoderm","Mesoderm") barplot(table,ylim=c(0,100),col="green")
- Layer specific MHBs with hyper-MHL
Ectoderm Endoderm Mesoderm 99 66 9
region | group | GSI |
chr8:29387092-29387216 | Ectoderm | 0.659537333117352 |
chr19:39898750-39898769 | Ectoderm | 0.622260349526761 |
chr11:120095770-120095841 | Ectoderm | 0.638436015070805 |
chr8:143298766-143298852 | Ectoderm | 0.629089907645855 |
chr16:21657412-21657574 | Ectoderm | 0.6376721097517 |
chr5:92934330-92934406 | Ectoderm | 0.667334656563231 |
chr3:43811289-43811331 | Ectoderm | 0.658785740481031 |
chr17:8601976-8601988 | Ectoderm | 0.602106513421994 |
chr10:121030613-121030661 | Ectoderm | 0.620355461223933 |
chr1:193377965-193378092 | Ectoderm | 0.612384341440121 |
chr18:13138062-13138194 | Ectoderm | 0.630293124544825 |
chr11:128065158-128065181 | Ectoderm | 0.615776035999425 |
chr7:115995198-115995218 | Ectoderm | 0.639634173881391 |
chr2:3583886-3583967 | Ectoderm | 0.629371815688128 |
chr21:24503682-24503775 | Ectoderm | 0.60393446974352 |
chr8:42750431-42750654 | Ectoderm | 0.609058674400317 |
chr1:22259946-22260017 | Ectoderm | 0.600124624290291 |
chr5:106878574-106878620 | Ectoderm | 0.609389311058491 |
chr10:123496262-123496391 | Ectoderm | 0.633479349721013 |
chr9:97713223-97713340 | Ectoderm | 0.602639172712739 |
chr6:43670518-43670599 | Ectoderm | 0.616096733986403 |
chr11:36706919-36707044 | Ectoderm | 0.639962708993761 |
chr15:42187197-42187218 | Ectoderm | 0.607623926207222 |
chr2:65804207-65804281 | Ectoderm | 0.603236104868574 |
chr17:77766959-77766979 | Ectoderm | 0.66624153932879 |
chr1:159893108-159893168 | Ectoderm | 0.671409324490059 |
chr2:121495455-121495544 | Ectoderm | 0.616705504439262 |
chr8:19522859-19522941 | Ectoderm | 0.61492324445635 |
chr19:38886666-38886702 | Ectoderm | 0.670488181288092 |
chr1:41849182-41849197 | Ectoderm | 0.601497796230824 |
chr19:38886138-38886153 | Ectoderm | 0.60215755360785 |
chr11:110065132-110065260 | Ectoderm | 0.620350268299807 |
chr18:28827952-28828043 | Ectoderm | 0.62733392232416 |
chr2:110438251-110438428 | Ectoderm | 0.609815651189271 |
chr11:74854298-74854413 | Ectoderm | 0.604758661736277 |
chr20:43966567-43966613 | Ectoderm | 0.633100005220329 |
chr2:85811833-85811846 | Ectoderm | 0.603742595694347 |
chr7:101961892-101961907 | Ectoderm | 0.636479562937856 |
chr22:19710901-19710936 | Ectoderm | 0.643860942397404 |
chr17:76732402-76732485 | Ectoderm | 0.630309428917436 |
chr16:88837350-88837417 | Ectoderm | 0.639956789529288 |
chr20:49262297-49262329 | Ectoderm | 0.62648816520905 |
chr1:186181479-186181655 | Ectoderm | 0.605638208915313 |
chr8:134203271-134203327 | Ectoderm | 0.620493153208632 |
chr5:169894194-169894243 | Ectoderm | 0.633726208035661 |
chr5:150403465-150403482 | Ectoderm | 0.62441239036749 |
chr9:137220495-137220592 | Ectoderm | 0.600899351123174 |
chr2:74209501-74209580 | Ectoderm | 0.602032376155113 |
chr20:5059205-5059233 | Ectoderm | 0.612938330332136 |
chr1:227545247-227545308 | Ectoderm | 0.609135849889118 |
chr7:33080614-33080718 | Ectoderm | 0.639600512160286 |
chr1:59362446-59362543 | Ectoderm | 0.619376367184664 |
chr2:203037243-203037337 | Ectoderm | 0.625115647207567 |
chr17:77767155-77767186 | Ectoderm | 0.638533123496661 |
chr7:43214618-43214840 | Ectoderm | 0.600723642889573 |
chr2:71644560-71644595 | Ectoderm | 0.641067698816342 |
chr7:139529310-139529349 | Ectoderm | 0.6134098285564 |
chr1:196946446-196946570 | Ectoderm | 0.610806427586173 |
chr2:42277283-42277335 | Ectoderm | 0.628058759527649 |
chr11:123016107-123016154 | Ectoderm | 0.657923031208003 |
chr1:229978819-229978864 | Ectoderm | 0.623894630744394 |
chr17:57078908-57079003 | Ectoderm | 0.610926283216838 |
chr7:22617356-22617407 | Ectoderm | 0.667929987625616 |
chr7:2757237-2757316 | Ectoderm | 0.601252252195626 |
chr3:36949925-36949965 | Ectoderm | 0.662948818910667 |
chr1:59361425-59361492 | Ectoderm | 0.658198739198946 |
chr21:40138947-40139045 | Ectoderm | 0.641545688027849 |
chr22:33018091-33018133 | Ectoderm | 0.605395609371496 |
chr10:45916330-45916353 | Ectoderm | 0.627360449725662 |
chr6:154975205-154975246 | Ectoderm | 0.607656376219889 |
chr21:34659414-34659513 | Ectoderm | 0.614947673577016 |
chr12:113065670-113065803 | Ectoderm | 0.637109038086428 |
chr11:61456495-61456567 | Ectoderm | 0.603736020447996 |
chr1:204592540-204592575 | Ectoderm | 0.600751451839705 |
chr22:38614662-38614758 | Ectoderm | 0.65680933946711 |
chr17:76588327-76588445 | Ectoderm | 0.655514821551318 |
chr16:86417535-86417723 | Ectoderm | 0.621362797865302 |
chr6:159128335-159128360 | Ectoderm | 0.648877652085264 |
chr3:167073066-167073152 | Ectoderm | 0.648045424921539 |
chr3:186928712-186928778 | Ectoderm | 0.610146996868578 |
chr11:57089649-57089743 | Ectoderm | 0.62677395784954 |
chr6:111239079-111239184 | Ectoderm | 0.63037773416189 |
chr17:48764127-48764188 | Ectoderm | 0.60627221893251 |
chr6:168197479-168197510 | Ectoderm | 0.632032999449708 |
chr15:74671324-74671459 | Ectoderm | 0.623154091775709 |
chr19:58868085-58868120 | Ectoderm | 0.674814055759394 |
chr4:153878727-153878844 | Ectoderm | 0.62419394200263 |
chr3:172280812-172280854 | Ectoderm | 0.625528145281659 |
chr3:122640840-122640863 | Ectoderm | 0.606059008480575 |
chr1:8064972-8064983 | Ectoderm | 0.644939000855723 |
chr12:248974-249014 | Ectoderm | 0.657233142275506 |
chr19:16272368-16272434 | Ectoderm | 0.610474524921455 |
chr5:132444216-132444275 | Ectoderm | 0.602807461907881 |
chr15:31890779-31891030 | Ectoderm | 0.603133103058883 |
chr21:45579708-45579771 | Ectoderm | 0.612035579928314 |
chr22:24906975-24907189 | Ectoderm | 0.604317977687824 |
chr21:45304017-45304067 | Ectoderm | 0.615161807537595 |
chr17:76732735-76732773 | Ectoderm | 0.627406271009881 |
chr20:21250244-21250339 | Ectoderm | 0.607049177788986 |
chr17:2119276-2119367 | Endoderm | 0.621555865969221 |
chr1:1957051-1957084 | Endoderm | 0.602650908155007 |
chr9:35689643-35689690 | Endoderm | 0.619387701280056 |
chr2:47241811-47241842 | Endoderm | 0.662829312044627 |
chr5:172305920-172305935 | Endoderm | 0.670739265276362 |
chr14:38080580-38080592 | Endoderm | 0.639966474713107 |
chr1:230476437-230476574 | Endoderm | 0.635030322574557 |
chr10:104575592-104575618 | Endoderm | 0.609149408140753 |
chr8:12957933-12957984 | Endoderm | 0.643490818086236 |
chr5:151043109-151043181 | Endoderm | 0.680177807411657 |
chr4:7632491-7632709 | Endoderm | 0.652423230457514 |
chr19:3670199-3670225 | Endoderm | 0.634998241133357 |
chr7:114584954-114585002 | Endoderm | 0.603616478692203 |
chr1:234669276-234669303 | Endoderm | 0.616809574818785 |
chr16:22229894-22229955 | Endoderm | 0.607629291159365 |
chr10:6216405-6216443 | Endoderm | 0.602971624717696 |
chr9:124615379-124615452 | Endoderm | 0.633955823125635 |
chr2:37875819-37875959 | Endoderm | 0.602628500656313 |
chr2:64242660-64242800 | Endoderm | 0.60726399310844 |
chr2:242101288-242101347 | Endoderm | 0.608076333824482 |
chr16:1560025-1560087 | Endoderm | 0.651972214196267 |
chr11:118081886-118081999 | Endoderm | 0.6029309710898 |
chr6:157372211-157372306 | Endoderm | 0.634278618167255 |
chr11:65683490-65683558 | Endoderm | 0.636307514242888 |
chr18:46316989-46317041 | Endoderm | 0.624166723941027 |
chr16:10832062-10832121 | Endoderm | 0.611440520083738 |
chr8:1811724-1811734 | Endoderm | 0.604615438333278 |
chr22:44759564-44759570 | Endoderm | 0.610192616512951 |
chr11:107906691-107906721 | Endoderm | 0.605751844696818 |
chr2:239358562-239358706 | Endoderm | 0.614617410007429 |
chr1:25062843-25062863 | Endoderm | 0.670823332436485 |
chr4:37624974-37625026 | Endoderm | 0.6544427274209 |
chr19:36642990-36643069 | Endoderm | 0.656605450961024 |
chr12:6664139-6664180 | Endoderm | 0.669123041535702 |
chr11:44161686-44161822 | Endoderm | 0.628887015251611 |
chr7:459050-459072 | Endoderm | 0.60012029687524 |
chr19:39154668-39154690 | Endoderm | 0.663027710309978 |
chr17:66511557-66511576 | Endoderm | 0.631028220970854 |
chr11:47629283-47629316 | Endoderm | 0.634080728472571 |
chr22:34271616-34271645 | Endoderm | 0.615941002445972 |
chr1:225954691-225954718 | Endoderm | 0.601078618642703 |
chr11:46732432-46732450 | Endoderm | 0.632603084148886 |
chr4:151504919-151504983 | Endoderm | 0.621077562503555 |
chr11:24086083-24086150 | Endoderm | 0.608691231029366 |
chr22:18335966-18336049 | Endoderm | 0.670754545443272 |
chr19:18761285-18761327 | Endoderm | 0.68028737010478 |
chr5:54887639-54887649 | Endoderm | 0.652970324942108 |
chr9:93682361-93682514 | Endoderm | 0.665920831412597 |
chr3:170893533-170893551 | Endoderm | 0.603621933335352 |
chr3:171024840-171024914 | Endoderm | 0.636779220273703 |
chr14:59894932-59895017 | Endoderm | 0.61228529088177 |
chr2:1656976-1657034 | Endoderm | 0.618587759655055 |
chr16:69961433-69961448 | Endoderm | 0.631835214629571 |
chr14:102394447-102394465 | Endoderm | 0.612365707941321 |
chr7:6202081-6202133 | Endoderm | 0.611591150947358 |
chr19:38664210-38664243 | Endoderm | 0.602726833114876 |
chr1:10292194-10292416 | Endoderm | 0.653640769186138 |
chr20:19357121-19357136 | Endoderm | 0.654714700397522 |
chr2:204553596-204553702 | Endoderm | 0.601402898925884 |
chr6:157469645-157469672 | Endoderm | 0.6380499171651 |
chr10:115386647-115386737 | Endoderm | 0.622056663225908 |
chr2:240234683-240234705 | Endoderm | 0.612158498128861 |
chr19:15514987-15514998 | Endoderm | 0.601666018050405 |
chr2:109196275-109196451 | Endoderm | 0.634236535885808 |
chr12:109240568-109240631 | Endoderm | 0.614972599326848 |
chr13:42188452-42188507 | Endoderm | 0.604875957545443 |
chr16:85394306-85394334 | Mesoderm | 0.603027122263449 |
chr14:34493536-34493559 | Mesoderm | 0.661457016899424 |
chr17:79322621-79322654 | Mesoderm | 0.609437589321225 |
chr11:655465-655517 | Mesoderm | 0.638631266023567 |
chr9:4664295-4664543 | Mesoderm | 0.622455538468081 |
chr11:117684083-117684169 | Mesoderm | 0.614193089173044 |
chr17:80847496-80847545 | Mesoderm | 0.614992470215796 |
chr5:158879531-158879581 | Mesoderm | 0.631390177181746 |
chr11:34847402-34847459 | Mesoderm | 0.657593838020926 |
Layer specific hypo-MHL regions (LSMHB)[edit]
- code in Genome-miner
library("impute") RawNARemove<-function(data,missratio=0.3){ threshold<-(missratio)*dim(data)[2] NaRaw<-which(apply(data,1,function(x) sum(is.na(x))>threshold)) zero<-which(apply(data,1,function(x) all(x==0))==T) NaRAW<-c(NaRaw,zero) if(length(NaRAW)>0){ dat<-data[-NaRAW,] }else{ dat<-data; } dat } ################################################################################################################### setwd("/home/shg047/monod/dec") infile="WGBS_methHap_load_matrix_20Oct2015.txt"; file1<-read.table(infile,head=T,sep="\t",row.names=1,as.is=T,check.names=F) # miss value detection and imputation library("impute") f2<-RawNARemove(file1,missratio=0.3) f2<-impute.knn(data.matrix(f2))$data colnames(f2) library("preprocessCore") f2.t1<-normalize.quantiles(f2[,13:58]) library("sva") batch=c(rep(1,10),rep(2,36)) f2.t2<-ComBat(f2.t1, batch, mod=NULL, par.prior = TRUE,prior.plots = FALSE) f2[,13:58]<-f2.t2 # re-assign colnames colnames(f2) colnames(f2)<-gsub("_","-",colnames(f2)) colname2<-unlist(lapply(colnames(f2),function(x) unlist(strsplit(x,"[.]"))[1])) colname2 colnames(f2)<-colname2 # be sure all the sample information has been stored in the following database saminfo2<-read.table("/home/shg047/monod/phase2/newsaminfo.txt",head=T,sep="\t",as.is=T) saminfo2<-saminfo2[match(colname2,saminfo2[,1]),] saminfo2 colnames(f2)<-saminfo2[,2] saminfo3<-read.table("/home/shg047/monod/saminfo/tissue2Layer.txt",head=T,sep="\t",as.is=T) f2<-f2[,saminfo2[,2] %in% saminfo3[,1]] fn<-f2 colnames(fn)<-saminfo3[match(colnames(fn),saminfo3[,1]),2] group=names(table(colnames(fn))) index=colnames(fn) gsi<-c() gmaxgroup<-c() pvalue=apply(fn,1,function(x) summary(aov(x~index))1[["Pr(>F)"]][1]) # R list will not be correctly shown in wiki, you can see raw script in edit mode pvalue=apply(fn,1,function(x) summary(aov(x~index))15[1]) # R list will not be correctly shown in wiki, you can see raw script in edit mode SigDiffMHBANOVA<-fn[match(names(which(pvalue<9.223561e-07)),rownames(fn)),] save(SigDiffMHBANOVA,file="SigDiffMHBANOVA.RData") setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl\\anova") library("gplots") load("SigDiffMHBANOVA.RData") SigDiffMHBANOVA[SigDiffMHBANOVA<0]<-0 SigDiffMHBANOVA[SigDiffMHBANOVA>1]<-1 SigDiffMHBANOVA<-SigDiffMHBANOVA[,order(colnames(SigDiffMHBANOVA))] pdf("Figure.supervised.layer.mhl.single.cpg.heatmap.analysis.combat.quantile.pdf") col=colorRampPalette(c("yellow", "blue"))(20) rlt<-heatmap.2(data.matrix(SigDiffMHBANOVA),col=col,trace="none",density.info="none",Colv=T,Rowv=T,key=T,keysize=1,cexCol=0.65,cexRow=0.15) dev.off()
- Layer specific MHBs with hypo-MHL
# Endoderm specific MHB with hypo-MHL chr11:16023703−16023847 chr8:131774761−131774884 chr7:100540088−100540103 chr5:10746894−10747078 chr14:69095543−69095569 chr1:120333406−120333474 chr4:185071507−185071556 chr15:63682373−63682439 chr6:136869788−136869917 chr15:69854565−69854745 chr2:235372763−235372775 chr7:150074899−150075088 chr11:86716322−86716463 chr10:125866028−125866205 chr20:51697944−51698112 chr11:45670341−45670390 chr13:107772692−107772845 # Mesoderm specific MHB with hypo-MHL chr2:227555394−227555409 chr14:38091850−38091925 chr14:38080503−38080551 chr7:99984750−99984849 chr4:55650506−55650562 chr10:13726663−13726680 chr2:204553596−204553702 chr14:38080580−38080592 chr9:137296113−137296129 chr12:6664139−6664180 chr5:151043109−151043181 chr19:39154699−39154740 chr6:157469645−157469672 chr19:36642990−36643069 chr11:68695417−68695433 chr19:39154668−39154690 chr3:114343145−114343262 chr2:109196275−109196451 chr8:61764645−61764654 chr4:140737662−140737678 chr7:116409578−116409798 chr2:30574091−30574117 # Ectoderm specific MHB with hypo-MHL chr20:32010750−32010885 chr4:56238469−56238664 chr12:15759107−15759119 chr2:27268131−27268232 chr15:43812034−43812191 chr2:118688440−118688576 chr7:141359663−141359879 chr8:9954912−9955067 chr9:92683370−92683559 chr2:201964657−201964684 chr1:93623462−93623507 chr3:142199628−142199667 chr5:118285675−118285700 chr8:95745542−95745573 chr6:107096030−107096062
- TFBS
for i in `ls /home/shg047/db/hg19/encode/encode.*.hg19.bed` do bedtools window -w 100 -a endo.mhb.hypo.bed -b $i >> endo.mhb.hypo.tf bedtools window -w 100 -a meso.mhb.hypo.bed -b $i >> meso.mhb.hypo.tf bedtools window -w 100 -a ecto.mhb.hypo.bed -b $i >> ecto.mhb.hypo.tf done cat endo.mhb.hypo.tf | awk '{print $4}' | sort -u > endo.mhb.hypo.uni.tf cat meso.mhb.hypo.tf | awk '{print $4}' | sort -u > meso.mhb.hypo.uni.tf cat ecto.mhb.hypo.tf | awk '{print $4}' | sort -u > ecto.mhb.hypo.uni.tf
- File Address in Genome-miner
/home/shg047/monod/layer/endo.mhb.hypo.bed /home/shg047/monod/layer/meso.mhb.hypo.bed /home/shg047/monod/layer/ecto.mhb.hypo.bed
- Venn graph
- Gene Ontolgoy
- Endoderm
Category | Term | Count | % | PValue | Fold Enrichment | FDR |
GOTERM_MF_FAT | GO:0003700~transcription factor activity | 26 | 86.66666667 | 1.02E-24 | 11.54044444 | 1.08E-21 |
SP_PIR_KEYWORDS | dna-binding | 27 | 90 | 1.08E-23 | 9.267398287 | 1.06E-20 |
SP_PIR_KEYWORDS | transcription regulation | 27 | 90 | 8.77E-23 | 8.544669299 | 8.59E-20 |
SP_PIR_KEYWORDS | Transcription | 27 | 90 | 1.55E-22 | 8.359005311 | 1.51E-19 |
GOTERM_MF_FAT | GO:0030528~transcription regulator activity | 27 | 90 | 1.10E-21 | 7.72797619 | 1.16E-18 |
GOTERM_MF_FAT | GO:0003677~DNA binding | 29 | 96.66666667 | 2.73E-20 | 5.384055484 | 2.88E-17 |
SP_PIR_KEYWORDS | nucleus | 30 | 100 | 1.12E-19 | 4.491010974 | 1.10E-16 |
GOTERM_BP_FAT | GO:0006350~transcription | 27 | 90 | 1.82E-18 | 5.794954783 | 2.67E-15 |
GOTERM_BP_FAT | GO:0045449~regulation of transcription | 28 | 93.33333333 | 1.10E-17 | 4.854338075 | 1.62E-14 |
GOTERM_MF_FAT | GO:0043565~sequence-specific DNA binding | 18 | 60 | 5.83E-16 | 12.83327842 | 5.88E-13 |
GOTERM_BP_FAT | GO:0006355~regulation of transcription, DNA-dependent | 24 | 80 | 9.18E-16 | 6.104004512 | 1.31E-12 |
GOTERM_BP_FAT | GO:0051252~regulation of RNA metabolic process | 24 | 80 | 1.62E-15 | 5.969332598 | 2.45E-12 |
SP_PIR_KEYWORDS | activator | 13 | 43.33333333 | 4.59E-12 | 16.02916667 | 4.50E-09 |
SP_PIR_KEYWORDS | DNA binding | 11 | 36.66666667 | 3.88E-11 | 20.74362745 | 3.80E-08 |
GOTERM_BP_FAT | GO:0006357~regulation of transcription from RNA polymerase II promoter | 14 | 46.66666667 | 8.55E-10 | 8.683723063 | 1.26E-06 |
GOTERM_CC_FAT | GO:0031981~nuclear lumen | 13 | 43.33333333 | 5.12E-09 | 6.741014199 | 5.27E-06 |
GOTERM_BP_FAT | GO:0010628~positive regulation of gene expression | 12 | 40 | 1.43E-08 | 9.313597246 | 2.10E-05 |
GOTERM_MF_FAT | GO:0003702~RNA polymerase II transcription factor activity | 9 | 30 | 4.24E-08 | 15.96270492 | 4.47E-05 |
GOTERM_CC_FAT | GO:0070013~intracellular organelle lumen | 13 | 43.33333333 | 5.40E-08 | 5.494362332 | 5.55E-05 |
GOTERM_CC_FAT | GO:0043233~organelle lumen | 13 | 43.33333333 | 7.00E-08 | 5.370588235 | 7.20E-05 |
GOTERM_MF_FAT | GO:0008134~transcription factor binding | 11 | 36.66666667 | 8.65E-08 | 9.279597141 | 9.12E-05 |
GOTERM_CC_FAT | GO:0031974~membrane-enclosed lumen | 13 | 43.33333333 | 8.76E-08 | 5.266417343 | 9.01E-05 |
GOTERM_BP_FAT | GO:0045941~positive regulation of transcription | 11 | 36.66666667 | 1.43E-07 | 8.794799054 | 2.11E-04 |
GOTERM_BP_FAT | GO:0045935~positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 11 | 36.66666667 | 3.67E-07 | 7.949145299 | 5.39E-04 |
GOTERM_BP_FAT | GO:0045893~positive regulation of transcription, DNA-dependent | 10 | 33.33333333 | 4.17E-07 | 9.453529001 | 6.13E-04 |
GOTERM_BP_FAT | GO:0051254~positive regulation of RNA metabolic process | 10 | 33.33333333 | 4.47E-07 | 9.374913375 | 6.58E-04 |
GOTERM_BP_FAT | GO:0051173~positive regulation of nitrogen compound metabolic process | 11 | 36.66666667 | 4.91E-07 | 7.702277433 | 7.21E-04 |
GOTERM_BP_FAT | GO:0010557~positive regulation of macromolecule biosynthetic process | 11 | 36.66666667 | 5.65E-07 | 7.584505607 | 8.31E-04 |
GOTERM_BP_FAT | GO:0010604~positive regulation of macromolecule metabolic process | 12 | 40 | 7.44E-07 | 6.31411902 | 0.001094283 |
GOTERM_BP_FAT | GO:0045944~positive regulation of transcription from RNA polymerase II promoter | 9 | 30 | 7.69E-07 | 10.93908356 | 0.001130801 |
GOTERM_BP_FAT | GO:0031328~positive regulation of cellular biosynthetic process | 11 | 36.66666667 | 8.65E-07 | 7.241265207 | 0.001271592 |
GOTERM_BP_FAT | GO:0009891~positive regulation of biosynthetic process | 11 | 36.66666667 | 9.87E-07 | 7.137074341 | 0.001451883 |
GOTERM_BP_FAT | GO:0010551~regulation of specific transcription from RNA polymerase II promoter | 6 | 20 | 1.51E-06 | 28.78297872 | 0.002226717 |
GOTERM_MF_FAT | GO:0046983~protein dimerization activity | 10 | 33.33333333 | 1.71E-06 | 7.984624846 | 0.001801204 |
INTERPRO | IPR004827:Basic-leucine zipper (bZIP) transcription factor | 5 | 16.66666667 | 2.04E-06 | 52.38679245 | 0.002102847 |
GOTERM_MF_FAT | GO:0016563~transcription activator activity | 9 | 30 | 2.21E-06 | 9.499756098 | 0.002335511 |
UP_SEQ_FEATURE | DNA-binding region:Basic motif | 6 | 20 | 4.02E-06 | 23.74285714 | 0.004570435 |
SMART | SM00338:BRLZ | 5 | 16.66666667 | 8.44E-06 | 35.68789308 | 0.006326719 |
GOTERM_BP_FAT | GO:0032583~regulation of gene-specific transcription | 6 | 20 | 8.68E-06 | 20.19104478 | 0.0127626 |
UP_SEQ_FEATURE | domain:Leucine-zipper | 5 | 16.66666667 | 2.21E-05 | 28.95909091 | 0.025103574 |
GOTERM_BP_FAT | GO:0006351~transcription, DNA-dependent | 7 | 23.33333333 | 3.00E-05 | 10.81004566 | 0.044147909 |
GOTERM_BP_FAT | GO:0032774~RNA biosynthetic process | 7 | 23.33333333 | 3.24E-05 | 10.66396396 | 0.047654411 |
SP_PIR_KEYWORDS | repressor | 7 | 23.33333333 | 3.95E-05 | 10.31762452 | 0.038665521 |
UP_SEQ_FEATURE | zinc finger region:NR C4-type | 4 | 13.33333333 | 4.27E-05 | 56.63111111 | 0.048544142 |
UP_SEQ_FEATURE | DNA-binding region:Nuclear receptor | 4 | 13.33333333 | 4.27E-05 | 56.63111111 | 0.048544142 |
- Mesoderm
Category | Term | Count | % | PValue | Fold Enrichment | FDR |
SP_PIR_KEYWORDS | transcription regulation | 12 | 92.30769231 | 1.87E-10 | 8.763763384 | 1.64E-07 |
SP_PIR_KEYWORDS | Transcription | 12 | 92.30769231 | 2.38E-10 | 8.573338781 | 2.08E-07 |
GOTERM_BP_FAT | GO:0045449~regulation of transcription | 12 | 92.30769231 | 1.30E-08 | 5.201076509 | 1.72E-05 |
SP_PIR_KEYWORDS | nucleus | 13 | 100 | 1.47E-08 | 4.491010974 | 1.28E-05 |
GOTERM_MF_FAT | GO:0016564~transcription repressor activity | 7 | 53.84615385 | 8.27E-08 | 23.96650844 | 8.10E-05 |
GOTERM_MF_FAT | GO:0030528~transcription regulator activity | 10 | 76.92307692 | 1.70E-07 | 7.15553351 | 1.67E-04 |
GOTERM_BP_FAT | GO:0016481~negative regulation of transcription | 7 | 53.84615385 | 5.90E-07 | 17.19244735 | 7.77E-04 |
GOTERM_BP_FAT | GO:0010629~negative regulation of gene expression | 7 | 53.84615385 | 1.02E-06 | 15.65740741 | 0.001345482 |
GOTERM_BP_FAT | GO:0045934~negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 7 | 53.84615385 | 1.12E-06 | 15.41276042 | 0.001475649 |
GOTERM_BP_FAT | GO:0051172~negative regulation of nitrogen compound metabolic process | 7 | 53.84615385 | 1.21E-06 | 15.20488118 | 0.001597891 |
GOTERM_MF_FAT | GO:0008134~transcription factor binding | 7 | 53.84615385 | 1.44E-06 | 14.76299545 | 0.001412732 |
GOTERM_BP_FAT | GO:0010558~negative regulation of macromolecule biosynthetic process | 7 | 53.84615385 | 1.65E-06 | 14.42656917 | 0.002173387 |
GOTERM_BP_FAT | GO:0031327~negative regulation of cellular biosynthetic process | 7 | 53.84615385 | 1.92E-06 | 14.06654783 | 0.002519407 |
GOTERM_BP_FAT | GO:0006350~transcription | 10 | 76.92307692 | 2.11E-06 | 5.365698874 | 0.002778119 |
GOTERM_BP_FAT | GO:0009890~negative regulation of biosynthetic process | 7 | 53.84615385 | 2.17E-06 | 13.77196044 | 0.002850924 |
GOTERM_CC_FAT | GO:0005654~nucleoplasm | 7 | 53.84615385 | 2.64E-06 | 11.27160494 | 0.002668839 |
SP_PIR_KEYWORDS | repressor | 6 | 46.15384615 | 4.02E-06 | 20.40848806 | 0.003505542 |
GOTERM_CC_FAT | GO:0044451~nucleoplasm part | 6 | 46.15384615 | 7.61E-06 | 15.35375375 | 0.007709187 |
GOTERM_BP_FAT | GO:0010605~negative regulation of macromolecule metabolic process | 7 | 53.84615385 | 9.13E-06 | 10.75113533 | 0.012014286 |
GOTERM_BP_FAT | GO:0006355~regulation of transcription, DNA-dependent | 9 | 69.23076923 | 9.79E-06 | 5.72250423 | 0.012881602 |
GOTERM_BP_FAT | GO:0051252~regulation of RNA metabolic process | 9 | 69.23076923 | 1.16E-05 | 5.596249311 | 0.015267288 |
UP_SEQ_FEATURE | domain:Leucine-zipper | 4 | 30.76923077 | 3.93E-05 | 53.46293706 | 0.04077532 |
SP_PIR_KEYWORDS | dna-binding | 8 | 61.53846154 | 4.11E-05 | 6.336682589 | 0.035859411 |
GOTERM_CC_FAT | GO:0031981~nuclear lumen | 7 | 53.84615385 | 4.82E-05 | 6.856245211 | 0.04883162 |